sanger_script

Script for sanger sequencing files delivery.

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

sars-cov2_analysis

Documentation for analyzing SARS-Cov2 samples.

sars_cov2_assembly-nf

Pipeline for analyzing sars-cov2 data using an de-novo assembly approximation

sars_cov2_consensus-nf

Nextflow pipeline to analyze SARS-Cov2 Illumina SISPA and/or amplicons data

scif_app_recipes

Install recipes for scif and Singularity/Docker containers

slides

taranis

cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.

test-datasets

Test data to be used for automated testing with the nf-core pipelines

trioanalysis-nf

Pipeline for trio family analysis. It accepts not only the ideal case with mother, father and affected, but also works for calling variants for incomplete trios, comparing more than one affected sibling and comparing with more relatives.

utils

General software scripts for sge usage

viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

virology_training

This repo contains all the resources needed to follow the virology training to analyze viral sequencing data.

wgmlst-nf

wgs-outbreaker

Pipeline for whole genome sequencing analysis for outbreak detection and characterization of foodborne bacteria